Wiki

Function

Plot amino acid properties of a protein sequence in parallel

Description

pepinfo plots various amino acid properties in parallel for an input protein sequence. The types of plot available are i. Hydrophobicity plots using the method of Kyte & Doolittle, the optimal matching hydrophobicity scale (OHM) of Sweet & Eisenberg, or consensus parameters (Eisenberg et al). ii. Histogram of the presence of residues with the physico-chemical properties: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charged, Positive, Negative. The data are also written out to an output file.

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

N

-warning

boolean

Report warnings

Boolean value Yes/No

Y

-error

boolean

Report errors

Boolean value Yes/No

Y

-fatal

boolean

Report fatal errors

Boolean value Yes/No

Y

-die

boolean

Report dying program messages

Boolean value Yes/No

Y

-version

boolean

Report version number and exit

Boolean value Yes/No

N

Input file format

pepinfo reads a single protein sequence.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.

The input format can be specified by using the
command-line qualifier -sformat xxx, where 'xxx' is replaced
by the name of the required format. The available format names are:
gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
(nbrf), swissprot (swiss, sw), dasgff and debug.

Output file format

The output is to the specified graphics device.

The results can be output in one of several formats by using the
command-line qualifier -graph xxx, where 'xxx' is replaced by
the name of the required device. Support depends on the availability
of third-party software packages.

Graphics File: pepinfo.ps

The output file 'pepinfo.out' contains the coordinates from the graphs.

For the first set of graphs, 9 sets of true/false values are written out.
For the second set of graphs, 3 sets of hydrophobicity values are written.

Data files

The physico-chemical properties of the residues are read from the EMBOSS
data file 'Eaa_properties.dat'. This file can be copied into your
current directory and inspected ot altered by using the application
'embossdata -fetch'. Another file can be specified using the qualifier
'-aaproperties'.

The hydropathy data of the residues are read from the EMBOSS data file
'Eaa_hydropathy.dat'. This file can be copied into your current
directory and inspected ot altered by using the application 'embossdata
-fetch'. Another file can be specified using the qualifier
'-aahydropathy'.

EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by EMBOSS environment variable EMBOSS_DATA.

Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

. (your current directory)

.embossdata (under your current directory)

~/ (your home directory)

~/.embossdata

Notes

For calculating the hydrophobicity plots, hdrophobicity is calculated in windows of a specified size over the sequence.

The optimal matching hydrophobicity scale (OHM) scale is based on the likelihood of a given amino acid to be replaced by another hydrophobic or "buried" amino acid.

References

Kyte J, Doolittle RF
A simple method for displaying the hydropathic character of a protein.
J Mol Biol 1982 May 5;157(1):105-132